/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __itkGradientDifferenceImageToImageMetric_hxx
#define __itkGradientDifferenceImageToImageMetric_hxx

#include "itkGradientDifferenceImageToImageMetric.h"
#include "itkImageRegionConstIteratorWithIndex.h"
#include "itkNumericTraits.h"

#include <iostream>
#include <iomanip>
#include <stdio.h>

#include "itkSimpleFilterWatcher.h"
namespace itk
{
/**
 * Constructor
 */
template< class TFixedImage, class TMovingImage >
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::GradientDifferenceImageToImageMetric()
{
  unsigned int iDimension;

  m_TransformMovingImageFilter = 0;

  for ( iDimension = 0; iDimension < FixedImageDimension; iDimension++ )
    {
    m_MinFixedGradient[iDimension] = 0;
    m_MaxFixedGradient[iDimension] = 0;

    m_Variance[iDimension] = 0;
    }

  for ( iDimension = 0; iDimension < MovedImageDimension; iDimension++ )
    {
    m_MinMovedGradient[iDimension] = 0;
    m_MaxMovedGradient[iDimension] = 0;
    }

  this->m_DerivativeDelta = 0.001;
}

/**
 * Initialize
 */
template< class TFixedImage, class TMovingImage >
void
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::Initialize(void)
throw ( ExceptionObject )
{
  unsigned int iFilter;  // Index of Sobel filters for each dimension

  if ( !this->GetComputeGradient() )
    {
    itkExceptionMacro(<< "Gradients must be calculated");
    }

  // Initialise the base class

  Superclass::Initialize();

  // Create the filter to resample the moving image

  m_TransformMovingImageFilter = TransformMovingImageFilterType::New();

  m_TransformMovingImageFilter->SetTransform(this->m_Transform);
  m_TransformMovingImageFilter->SetInterpolator(this->m_Interpolator);
  m_TransformMovingImageFilter->SetInput(this->m_MovingImage);

  m_TransformMovingImageFilter->SetDefaultPixelValue(0);

  m_TransformMovingImageFilter->SetSize( this->m_FixedImage->GetLargestPossibleRegion().GetSize() );
  m_TransformMovingImageFilter->SetOutputOrigin( this->m_FixedImage->GetOrigin() );
  m_TransformMovingImageFilter->SetOutputSpacing( this->m_FixedImage->GetSpacing() );
  m_TransformMovingImageFilter->SetOutputDirection( this->m_FixedImage->GetDirection() );

  // Compute the image gradients
  // ~~~~~~~~~~~~~~~~~~~~~~~~~~~

  // Compute the gradient of the fixed image

  m_CastFixedImageFilter = CastFixedImageFilterType::New();
  m_CastFixedImageFilter->SetInput(this->m_FixedImage);

  for ( iFilter = 0; iFilter < FixedImageDimension; iFilter++ )
    {
    m_FixedSobelOperators[iFilter].SetDirection(iFilter);
    m_FixedSobelOperators[iFilter].CreateDirectional();

    m_FixedSobelFilters[iFilter] = FixedSobelFilter::New();

    m_FixedSobelFilters[iFilter]->OverrideBoundaryCondition(&m_FixedBoundCond);
    m_FixedSobelFilters[iFilter]->SetOperator(m_FixedSobelOperators[iFilter]);

    m_FixedSobelFilters[iFilter]->SetInput( m_CastFixedImageFilter->GetOutput() );

    m_FixedSobelFilters[iFilter]->UpdateLargestPossibleRegion();
    }

  ComputeVariance();

  // Compute the gradient of the transformed moving image

  m_CastMovedImageFilter = CastMovedImageFilterType::New();
  m_CastMovedImageFilter->SetInput( m_TransformMovingImageFilter->GetOutput() );

  for ( iFilter = 0; iFilter < MovedImageDimension; iFilter++ )
    {
    m_MovedSobelOperators[iFilter].SetDirection(iFilter);
    m_MovedSobelOperators[iFilter].CreateDirectional();

    m_MovedSobelFilters[iFilter] = MovedSobelFilter::New();

    m_MovedSobelFilters[iFilter]->OverrideBoundaryCondition(&m_MovedBoundCond);
    m_MovedSobelFilters[iFilter]->SetOperator(m_MovedSobelOperators[iFilter]);

    m_MovedSobelFilters[iFilter]->SetInput( m_CastMovedImageFilter->GetOutput() );

    m_MovedSobelFilters[iFilter]->UpdateLargestPossibleRegion();
    }
}

/**
 * PrintSelf
 */
template< class TFixedImage, class TMovingImage >
void
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);
  os << indent << "DerivativeDelta: " << this->m_DerivativeDelta << std::endl;
}

/**
 * Compute the range of the moved image gradients
 */
template< class TFixedImage, class TMovingImage >
void
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::ComputeMovedGradientRange(void) const
{
  unsigned int           iDimension;
  MovedGradientPixelType gradient;

  for ( iDimension = 0; iDimension < FixedImageDimension; iDimension++ )
    {
    typedef itk::ImageRegionConstIteratorWithIndex<
      MovedGradientImageType > IteratorType;

    IteratorType iterate( m_MovedSobelFilters[iDimension]->GetOutput(),
                          this->GetFixedImageRegion() );

    gradient = iterate.Get();

    m_MinMovedGradient[iDimension] = gradient;
    m_MaxMovedGradient[iDimension] = gradient;

    while ( !iterate.IsAtEnd() )
      {
      gradient = iterate.Get();

      if ( gradient > m_MaxMovedGradient[iDimension] )
        {
        m_MaxMovedGradient[iDimension] = gradient;
        }

      if ( gradient < m_MinMovedGradient[iDimension] )
        {
        m_MinMovedGradient[iDimension] = gradient;
        }

      ++iterate;
      }
    }
}

/**
 * Compute the gradient variances in each dimension.
 */
template< class TFixedImage, class TMovingImage >
void
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::ComputeVariance(void) const
{
  unsigned int           iDimension;
  SizeValueType          nPixels;
  FixedGradientPixelType mean[FixedImageDimension];
  FixedGradientPixelType gradient;

  for ( iDimension = 0; iDimension < FixedImageDimension; iDimension++ )
    {
    typedef itk::ImageRegionConstIteratorWithIndex<
      FixedGradientImageType > IteratorType;

    IteratorType iterate( m_FixedSobelFilters[iDimension]->GetOutput(),
                          this->GetFixedImageRegion() );

    // Calculate the mean gradients

    nPixels =  0;

    gradient = iterate.Get();

    mean[iDimension] = 0;

    m_MinMovedGradient[iDimension] = gradient;
    m_MaxMovedGradient[iDimension] = gradient;

    while ( !iterate.IsAtEnd() )
      {
      gradient = iterate.Get();
      mean[iDimension] += gradient;

      if ( gradient > m_MaxFixedGradient[iDimension] )
        {
        m_MaxFixedGradient[iDimension] = gradient;
        }

      if ( gradient < m_MinFixedGradient[iDimension] )
        {
        m_MinFixedGradient[iDimension] = gradient;
        }

      nPixels++;
      ++iterate;
      }

    if ( nPixels > 0 )
      {
      mean[iDimension] /= nPixels;
      }

    // Calculate the variance

    iterate.GoToBegin();

    m_Variance[iDimension] = 0;

    while ( !iterate.IsAtEnd() )
      {
      gradient = iterate.Get();
      gradient -= mean[iDimension];

      m_Variance[iDimension] += gradient * gradient;

      ++iterate;
      }

    m_Variance[iDimension] /= nPixels;
    }
}

/**
 * Get the value of the similarity measure
 */
template< class TFixedImage, class TMovingImage >
typename GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >::MeasureType
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::ComputeMeasure(const TransformParametersType & parameters,
                 const double *subtractionFactor) const
{
  unsigned int iDimension;

  this->SetTransformParameters(parameters);
  m_TransformMovingImageFilter->UpdateLargestPossibleRegion();
  MeasureType measure = NumericTraits< MeasureType >::Zero;

  for ( iDimension = 0; iDimension < FixedImageDimension; iDimension++ )
    {
    if ( m_Variance[iDimension] == NumericTraits< MovedGradientPixelType >::Zero )
      {
      continue;
      }
    // Iterate over the fixed and moving gradient images
    // calculating the similarity measure

    MovedGradientPixelType movedGradient;
    FixedGradientPixelType fixedGradient;

    MovedGradientPixelType diff;

    typedef  itk::ImageRegionConstIteratorWithIndex< FixedGradientImageType >
    FixedIteratorType;

    FixedIteratorType fixedIterator( m_FixedSobelFilters[iDimension]->GetOutput(),
                                     this->GetFixedImageRegion() );

    typedef  itk::ImageRegionConstIteratorWithIndex< MovedGradientImageType >
    MovedIteratorType;

    MovedIteratorType movedIterator( m_MovedSobelFilters[iDimension]->GetOutput(),
                                     this->GetFixedImageRegion() );

    m_FixedSobelFilters[iDimension]->UpdateLargestPossibleRegion();
    m_MovedSobelFilters[iDimension]->UpdateLargestPossibleRegion();

    this->m_NumberOfPixelsCounted = 0;

    while ( !fixedIterator.IsAtEnd() )
      {
      // Get the moving and fixed image gradients

      movedGradient = movedIterator.Get();
      fixedGradient  = fixedIterator.Get();

      // And calculate the gradient difference

      diff = fixedGradient - subtractionFactor[iDimension] * movedGradient;

      measure += m_Variance[iDimension] / ( m_Variance[iDimension] + diff * diff );

      ++fixedIterator;
      ++movedIterator;
      }
    }

  return measure;
}

/**
 * Get the value of the similarity measure
 */
template< class TFixedImage, class TMovingImage >
typename GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >::MeasureType
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::GetValue(const TransformParametersType & parameters) const
{
  unsigned int iFilter;                        // Index of Sobel filters for
                                               // each dimension
  unsigned int iDimension;

  this->SetTransformParameters(parameters);
  m_TransformMovingImageFilter->UpdateLargestPossibleRegion();

  // Update the gradient images

  for ( iFilter = 0; iFilter < MovedImageDimension; iFilter++ )
    {
    m_MovedSobelFilters[iFilter]->UpdateLargestPossibleRegion();
    }

  // Compute the range of the moved image gradients
  // NB: Ideally this should be a filter as the computation is only
  //     required if the moved gradient image has been updated.
  //     However for the moment we'll assume that this is the case
  //     whenever GetValue() is called.

  this->ComputeMovedGradientRange();

  // Compute the similarity measure

  MovedGradientPixelType subtractionFactor[FixedImageDimension];
  MeasureType            currentMeasure;

  for ( iDimension = 0; iDimension < FixedImageDimension; iDimension++ )
    {
    subtractionFactor[iDimension] = 1.0;
    }

  // Compute the new value of the measure for this subtraction factor
  currentMeasure = this->ComputeMeasure(parameters, subtractionFactor);

  return currentMeasure;
}

/**
 * Get the Derivative Measure
 */
template< class TFixedImage, class TMovingImage >
void
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::GetDerivative(const TransformParametersType & parameters,
                DerivativeType & derivative) const
{
  TransformParametersType testPoint;

  testPoint = parameters;

  const unsigned int numberOfParameters = this->GetNumberOfParameters();
  derivative = DerivativeType(numberOfParameters);

  for ( unsigned int i = 0; i < numberOfParameters; i++ )
    {
    testPoint[i] -= this->m_DerivativeDelta;
    const MeasureType valuep0 = this->GetValue(testPoint);
    testPoint[i] += 2 * this->m_DerivativeDelta;
    const MeasureType valuep1 = this->GetValue(testPoint);
    derivative[i] = ( valuep1 - valuep0 ) / ( 2 * this->m_DerivativeDelta );
    testPoint[i] = parameters[i];
    }
}

/**
 * Get both the match Measure and theDerivative Measure
 */
template< class TFixedImage, class TMovingImage >
void
GradientDifferenceImageToImageMetric< TFixedImage, TMovingImage >
::GetValueAndDerivative(const TransformParametersType & parameters,
                        MeasureType & Value, DerivativeType  & Derivative) const
{
  Value      = this->GetValue(parameters);
  this->GetDerivative(parameters, Derivative);
}
} // end namespace itk

#endif
